Determining entire genomes of non-model organisms is becoming increasingly important in ecology and evolution research. High-throughput DNA sequencing technologies meanwhile allow the rapid generation of comprehensive genomic data from individual organisms, symbiotic associations, and even entire communities. However, assembling individual genomes from mixed species data sets followed by reliable gene predictions and annotations is still challenging. Here we use lichens as examples to devise strategies for such metagenomic approaches to eukaryote genome sequencing. We generate metagenome and metatranscriptome data for three lichen-forming fungi Lasallia pustulata, Pseudevernia furfuracea and Evernia prunastri, together with their trebouxioid green algal symbionts. Sequence analyses on real data are paired with simulation studies to evaluate individual approaches in a controlled framework. This study contributes to improving bioinformatics strategies to generating genomes of individual single organisms from metagenomic DNA.